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- PDB-3cax: Crystal structure of uncharacterized protein PF0695 -

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Basic information

Entry
Database: PDB / ID: 3cax
TitleCrystal structure of uncharacterized protein PF0695
ComponentsUncharacterized protein PF0695
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Domain of unknown function DUF438 / Family of unknown function (DUF438) / PAS domain / nmb1532 protein domain like / Hemerythrin-like / Hemerythrin HHE cation binding domain / PAS domain / Beta-Lactamase / Four Helix Bundle (Hemerythrin (Met), subunit A) / PAS domain superfamily ...Domain of unknown function DUF438 / Family of unknown function (DUF438) / PAS domain / nmb1532 protein domain like / Hemerythrin-like / Hemerythrin HHE cation binding domain / PAS domain / Beta-Lactamase / Four Helix Bundle (Hemerythrin (Met), subunit A) / PAS domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.43 Å
AuthorsRamagopal, U.A. / Hu, S. / Toro, R. / Gilmore, M. / Bain, K. / Meyer, A.J. / Rodgers, L. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein PF0695.
Authors: Ramagopal, U.A. / Hu, S. / Toro, R. / Gilmore, M. / Bain, K. / Meyer, A.J. / Rodgers, L. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein PF0695


Theoretical massNumber of molelcules
Total (without water)43,6141
Polymers43,6141
Non-polymers00
Water1,35175
1
A: Uncharacterized protein PF0695

A: Uncharacterized protein PF0695


Theoretical massNumber of molelcules
Total (without water)87,2292
Polymers87,2292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.840, 119.534, 181.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Uncharacterized protein PF0695


Mass: 43614.312 Da / Num. of mol.: 1 / Fragment: Residues 118-475
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Species: Pyrococcus furiosus / Strain: DSM 3638 / JCM 8422 / Vc1 / Gene: PF0695 / Plasmid: BC-pSGX4(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U2Y3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67.02 %
Description: The data set that was collected at the NSLS beamline X4C has been used for SAD
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Ammonium(tri-)citrate pH 7.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4C10.9793
SYNCHROTRONNSLS X29A20.979
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDFeb 1, 2008
ADSC QUANTUM 3152CCDJan 25, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.9791
ReflectionResolution: 2.43→50 Å / Num. all: 24050 / Num. obs: 24050 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.107 / Χ2: 1.116 / Net I/σ(I): 7.7
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.74 / Num. unique all: 2337 / Rsym value: 0.547 / Χ2: 0.567 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.43→34.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.852 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.248 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1234 5.1 %RANDOM
Rwork0.185 ---
all0.188 24031 --
obs0.188 24031 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.504 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2--0.4 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.43→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 0 75 3022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223030
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9854092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1445356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61724.097144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87415583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5631521
X-RAY DIFFRACTIONr_chiral_restr0.0780.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022265
X-RAY DIFFRACTIONr_nbd_refined0.2240.31213
X-RAY DIFFRACTIONr_nbtor_refined0.3170.52073
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.376
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.518
X-RAY DIFFRACTIONr_mcbond_it4.40321843
X-RAY DIFFRACTIONr_mcangle_it5.87632904
X-RAY DIFFRACTIONr_scbond_it5.57621361
X-RAY DIFFRACTIONr_scangle_it7.65631188
LS refinement shellResolution: 2.43→2.494 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 53 -
Rwork0.274 1008 -
all-1061 -
obs--58.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9235-1.61530.4964.5596-0.80160.8465-0.0248-0.2268-0.02470.25320.01660.22370.071-0.07120.0082-0.1908-0.04790.037-0.142-0.0011-0.171422.11730.84355.936
22.7455-0.3941-1.22972.520.106711.20430.0503-0.1582-0.1690.0653-0.0817-0.25810.95090.37970.03140.11810.0653-0.0389-0.0030.048-0.183533.81916.99485.644
32.3524-1.4242-0.74253.4976-0.78996.4236-0.2298-0.10110.62890.02170.20520.0321-1.0225-0.52710.02450.19350.1041-0.11040.0659-0.1064-0.062623.73330.408103.353
418.03414.9657-6.090831.70323.227718.77580.84190.16511.3741-0.0425-0.0448-0.5369-1.97970.0358-0.79710.1717-0.0464-0.06410.150.06350.178738.04745.30681.83
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA119 - 3345 - 220
2X-RAY DIFFRACTION2AA335 - 363221 - 249
3X-RAY DIFFRACTION3AA364 - 459250 - 345
4X-RAY DIFFRACTION4AA460 - 473346 - 359

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